Nucleotidic structures comprising N-4 derivatized pyrimidines have recently been discovered to be extremely useful in the chemical synthesis of linear and branched polynucleotide probes. For example, commonly assigned U.S. Pat. No. 4,910,300 to Urdea et al. describes probes made with modified nucleotides having the structure ##STR2## wherein R.sup.1 is a reactive group derivatizable with a detectable label, R.sup.2 is an optional linking group, R.sup.3 is hydrogen, methyl or halogen, is hydrogen or a capping or blocking group, R.sup.5 is hydrogen or a phosphorus derivative, and R.sup.6 is hydrogen or a protected or unprotected hydroxyl group. The polynucleotide probes described in the '300 patent are linear probes useful in a wide variety of hybridization assay formats, including that involving multi-component capturing and labelling systems as described in commonly assigned U.S. Pat. No. 4,868,105 to Urdea et al.
Such N-4 modified pyrimidine nucleotides have also been used to make branched polynucleotides, as described, for example, in commonly assigned U.S. Pat. No. 5,124,246 to Urdea et al. and in commonly assigned U.S. patent application Ser. No. 07/813,588 ("Large Comb-Type Branched Polynucleotides",inventors Urdea et al.). Both of these documents illustrate the utility of N-4 modified pyrimidine nucleotides in the synthesis of "nucleic acid multimers" or "amplification multimers," polynucleotides having a branched structure by virtue of containing three or more oligonucleotide units emanating from a single point of origin.
The present invention is directed to a new class of N-4 modified pyrimidine nucleotides useful in a variety of contexts, including the hybridization assays described in the aforementioned references. The new compounds may be readily synthesized using commercially available materials, are easily incorporated into polynucleotide probes using conventional synthetic methods, and lend themselves to use in conjunction with automated DNA synthesis equipment.